PDBsum entry 1i8j

Lyase

PDB id: 1i8j

Contents

Protein chains

323 a.a. *

Ligands

DSB ×2

Metals

_ZN ×2

_MG ×2

Waters ×316

* Residue conservation analysis

PDB id:

1i8j

Name:

Lyase

Title:

Crystal structure of porphobilinogen synthase complexed with the inhibitor 4,7-dioxosebacic acid

Structure:

Porphobilinogen synthase. Chain: a, b. Synonym: delta-aminolevulinic acid dehydratase, 5-aminolevulinic acid dehydratase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Octamer (from PDB file)

Resolution:

1.90Å R-factor: 0.198 R-free: 0.247

Authors:

J.Kervinen,E.K.Jaffe,F.Stauffer,R.Neier,A.Wlodawer,A.Zdanov

Key ref:

J.Kervinen et al. (2001). Mechanistic basis for suicide inactivation of porphobilinogen synthase by 4,7-dioxosebacic acid, an inhibitor that shows dramatic species selectivity. Biochemistry, 40, 8227-8236. PubMed id: 11444968 DOI: 10.1021/bi010656k

Date:

14-Mar-01 Release date: 20-Jun-01

Protein chains

P0ACB2  (HEM2_ECOLI) -  Delta-aminolevulinic acid dehydratase from Escherichia coli (strain K12)

Seq: 324 a.a.

Struc: 323 a.a.

Enzyme reactions

• Enzyme class: E.C.4.2.1.24 - porphobilinogen synthase.
• Pathway: Porphyrin Biosynthesis (early stages)
• Reaction: 2 5-aminolevulinate = porphobilinogen + 2 H2O + H⁺

2 × 5-aminolevulinate (Bound ligand (Het Group name = DSB) matches with 43.75% similarity) = porphobilinogen + 2 × H2O + H(+)

• Cofactor: Zn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1021/bi010656k

Biochemistry 40:8227-8236 (2001)

PubMed id: 11444968

Mechanistic basis for suicide inactivation of porphobilinogen synthase by 4,7-dioxosebacic acid, an inhibitor that shows dramatic species selectivity.

J.Kervinen, E.K.Jaffe, F.Stauffer, R.Neier, A.Wlodawer, A.Zdanov.

ABSTRACT

4,7-Dioxosebacic acid (4,7-DOSA) is an active site-directed irreversible inhibitor of porphobilinogen synthase (PBGS). PBGS catalyzes the first common step in the biosynthesis of the tetrapyrrole cofactors such as heme, vitamin B(12), and chlorophyll. 4,7-DOSA was designed as an analogue of a proposed reaction intermediate in the physiological PBGS-catalyzed condensation of two molecules of 5-aminolevulinic acid. As shown here, 4,7-DOSA exhibits time-dependent and dramatic species-specific inhibition of PBGS enzymes. IC(50) values vary from 1 microM to 2.4 mM for human, Escherichia coli, Bradyrhizobium japonicum, Pseudomonas aeruginosa, and pea enzymes. Those PBGS utilizing a catalytic Zn(2+) are more sensitive to 4,7-DOSA than those that do not. Weak inhibition of a human mutant PBGS establishes that the inactivation by 4,7-DOSA requires formation of a Schiff base to a lysine that normally forms a Schiff base intermediate to one substrate molecule. A 1.9 A resolution crystal structure of E. coli PBGS complexed with 4,7-DOSA (PDB code ) shows one dimer per asymmetric unit and reveals that the inhibitor forms two Schiff base linkages with each monomer, one to the normal Schiff base-forming Lys-246 and the other to a universally conserved "perturbing" Lys-194 (E. coli numbering). This is the first structure to show inhibitor binding at the second of two substrate-binding sites.